A federal court’s ruling Wednesday that Apple (AAPL) conspired to fix prices for e-books could end up being a costly and enduring headache for the company, which now faces the prospect of court-imposed penalties and class-action suits. The ruling could also lead to greater scrutiny of its other businesses from regulators.

“Now the Department of Justice is emboldened to continue to challenge what Apple does in the future, and so are the states,” said Max Huffman, an associate professor at Indiana University’s Robert H. McKinney School of Law and an expert on antitrust and consumer law.

U.S. District Judge Denise Cote in Manhattan ruled that Apple colluded with five of the six major book publishers to raise the prices that consumers pay for e-books. Citing damning emails from late Apple CEO Steve Jobs and other executives, Cote ruled that Apple, in the months before the launch of the first iPad, conspired with the publishers to undermine Amazon, then the dominant e-book seller, and ensure that there would be no price competition among e-book retailers.

Amazon remains the largest e-book seller, but a spokesman at Publishers Weekly said industry experts expect Apple will displace Barnes & Noble for the No. 2 spot by the end of the year.

Apple, which all along has denied the price-fixing charges, vowed to appeal the ruling. “Apple did not conspire to fix e-book pricing and we will continue to fight against these false accusations,” company spokesman Tom Neumayr said in an emailed statement.

The antitrust case will now move to a penalty phase. Apple is not at risk of having to pay a fine but will have federal regulators keeping close tabs on how it conducts business in the e-books market.

Also, separate lawsuits against Apple by some 33 state attorneys general will now go forward; several private consumer lawsuits already are underway. Those cases seek to recover for consumers the excess amounts they paid for e-books as a result of Apple’s conspiracy with the book publishers. If it loses those cases, Apple could pay triple damages.

Meanwhile, Apple could see regulatory scrutiny go well beyond e-books. The company has already come under fire for the degree of control it has in the digital music and smartphone apps markets and could see antitrust regulators scrutinizing those businesses more closely.

“Apple has to tread cautiously,” said Eric Goldman, a professor at Santa Clara University School of Law. “People are watching what they’re doing.”

The antitrust case stemmed from Apple’s desire to showcase the iPad as an e-reader when it launched the tablet in 2010. In the months before unveiling the device, Apple negotiated with the major book publishers to get the rights to sell e-books in iBookstore, a new digital bookstore it was creating for the device.

Amazon at the time bought e-books wholesale from the publishers and then set its own retail prices. But Apple agreed to sell e-books on an “agency” model, where the publishers would set prices of their books and Apple would simply take a 30 percent commission.

The agreements also included a so-called “most-favored nation” clause that allowed Apple to match the lowest prices offered by competing e-book stores. That imposed significant financial costs on the publishers if they didn’t force Amazon and other e-book sellers to switch over to an agency model like Apple’s.

Thanks to such provisions, prices of e-books skyrocketed after Apple’s iBookstore launched, rising in some cases by more than 50 percent, Cote said. On average, according to the Justice Department, e-book prices rose 18 percent.

“Those higher prices were not the result of regular market forces but of a scheme in which Apple was a full participant,” Cote wrote in her decision.

The Department of Justice, which previously secured settlements with the five publishers accused of conspiring with Apple, lauded Wednesday’s ruling.

“Companies cannot ignore the antitrust laws when they believe it is in their economic self-interest to do so,” Assistant Attorney General Bill Baer said in a statement. “This decision by the court is a critical step in undoing the harm caused by Apple’s illegal actions.”

Law experts say Apple’s chances of winning an appeal are slim. Appeals courts almost always defer to trial courts in cases such as these, which are based on a substantial amount of documented evidence.

Apple has built a reputation as an aggressive negotiator with companies that supply not just the books but the movies, music and other media sold on Apple iTunes. But the ruling may force it to rethink the way it does business with media companies and publishers, legal experts said.

Contact Troy Wolverton at 408-840-4285. Follow him at Twitter.com/troywolv.

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